tbuckley/cabot-search huggingface dataset:
Resynchronized rhythmic oscillations of gut microbiota drive time-restricted feeding induced nonalcoholic steatohepatitis alleviation
Authors: Jiafeng Xia, Wanru Guo, Ming Hu, Xiuyuan Jin, Sitong Zhang, Boqiang Liu, Hangyuan Qiu, Kaicen Wang, Aoxiang Zhuge, Shengjie Li, Zhongkang Ji, Lanjuan Li, Kaijin Xu
Journal: Gut Microbes (2023)

With the drive of the endogenous circadian clock and external cues such as feeding behavior, the microbial community generates rhythmic oscillations in composition and function. Microbial oscillations are crucial in orchestrating host metabolic homeostasis during the predictable 24-hour diurnal cycle. A time-restricted feeding (TRF) regimen is a promising dietary strategy to optimize energy utilization, alleviate metabolic syndrome and reinforce microbial cyclical fluctuations. However, the causative relationship between reinforced microbial rhythmicity and TRF-induced metabolic improvement remains elusive. In this study, we corroborated that the TRF regimen notably alleviated obesity and nonalcoholic steatohepatitis (NASH) with reinstated rhythmicity of genera such as Lactobacillus, Mucispirillum, Acetatifactor, and Lachnoclostridium. The reshaped microbial oscillations correlate with cyclical fluctuations in intestinal amino acids. Furthermore, fecal microbiota transplantation (FMT) indicated that only the TRF feeding phase-derived microbiota, but not the TRF fasting phase-derived microbiota, could protect mice from NASH and reinstate microbial rhythmicity, confirming that the microbiota improved NASH in a time-of-day-specific manner. The unique role of the TRF-feeding phase-derived microbiota was accompanied by regulation of the serotonergic synapse pathway and rejuvenation of the microbial production of indole derivatives. Our results revealed the discrepant characteristics between the feeding and fasting phases and the time-of-day-specific configuration of microbiota functionality in the TRF regimen.
Error in an Affiliation and Corresponding Author Address
Journal: JAMA Network Open (2023)

Nilakshi Vaidya, MSc; Bharath Holla, MD; Jon Heron, PhD; Eesha Sharma, MD; Yuning Zhang, PhD; Gwen Fernandes, PhD; Udita Iyengar, PhD; Alex Spiers, MSc; Anupa Yadav, MTech; Surajit Das, MSc; Sanjit Roy, BSc; Chirag K. Ahuja, MD; Gareth J. Barker, PhD; Debasish Basu, MD; Rose Dawn Bharath, DM; Matthew Hickman, PhD; Sanjeev Jain, MD; Kartik Kalyanram, MD; Kamakshi Kartik, MD; Murali Krishna, PhD; Ghattu Krishnaveni, PhD; Kalyanaraman Kumaran, DM; Rebecca Kuriyan, PhD; Pratima Murthy, MD; Dimitri Papadopoulos Orfanos, PhD; Meera Purushottam, PhD; Sunita Simon Kurpad, DNB; Lenin Singh, MD; Roshan Singh, PhD; B. N. Subodh, MD; Mireille Toledano, PhD; Henrik Walter, PhD; Sylvane Desrivières, PhD; Amit Chakrabarti, MD; Vivek Benegal, MD; Gunter Schumann, MD; Consortium on Vulnerability to Externalizing Disorders and Addictions (cVEDA) ; Mathew Varghese; Kandavel Thennarasu; Urvakhsh Metha; Satish Girimaji; Preeti Jacob; Deepak Jayarajan; Keshav Kumar; Gitanjali Narayanan; Madhu Khullar; Niranjan Khandelwal; Abhishek Ghosh; Nainesh Joshi; Ningthoujam Debala Chanu; Fujica M.C.; Victoria Ph.; Celina Phurailatpam; Debangana Bhattacharya; Bidisha Haque; Alisha Nagraj; Arpita Ghosh; Anirban Basu; Mriganka Pandit; Subhadip Das; Pawan Maurya; Amritha Gourisankar; Geetha Rani T; Sujatha B; Madhavi Rangaswamy; Caroline Fall; Kiran KN; Ramya MC; Chaitra Urs; Santhosh N; Somashekhara R; Divyashree K; Arathi Rao; Poornima R; Saswathika Tripathy; Neha Parashar; Nayana K B; Ashwini Seshadri; Sathish Kumar; Suneela Baligar; Thamodaran Arumugam; Apoorva Safai; Anthony Cyril; Ashika Roy; Dhanalakshmi D; Shivamma D; Bhavana B R
Content Analysis of Emoji and Emoticon Use in Clinical Texting Systems
Authors: Colin M. E. Halverson, Claire E. Donnelly, Michael Weiner, Joy L. Lee
Journal: JAMA Network Open (2023)

Importance Emoji and emoticons are quickly becoming an omnipresent feature of virtual communication. As health care systems increasingly adopt clinical texting applications, it is critical to understand how clinicians use these ideograms with colleagues and how it may affect their interactions. Objective To evaluate the functions that emoji and emoticons serve in clinical text messages. Design, Setting, and Participants This qualitative study’s content analysis of clinical text messages from a secure clinical messaging platform was conducted to assess the communicative function of emoji and emoticons. The analysis included messages sent by hospitalists to other health care clinicians. A subset of a random 1% sample of all message threads, which included at least 1 emoji or emoticon, on a clinical texting system used by a large, Midwestern US hospital from July 2020 until March 2021 were analyzed. A total of 80 hospitalists participated in the candidate threads. Main Outcomes Whether and what kind of emoji or emoticon was deployed in each reviewed thread was tabulated by the study team. The communicative function of each emoji and emoticon was assessed according to a prespecified coding scheme. Results A total of 80 hospitalists (49 [61%] male; 30 [37%] Asian, 5 [6%] Black or African American, 2 [3%] Hispanic or Latinx, 42 [53%] White; of 41 with age data, 13 [32%] aged 25-34 years, 19 [46%] aged 35-44 years) participated in the 1319 candidate threads. Within the sample of 1319 threads, 7% of threads (155 unique messages) contained at least 1 emoji or emoticon. The majority (94 [61%]) functioned emotively, that is, conveyed the internal state of the sender, and 49 (32%) served to open, maintain, or close communication. No evidence was identified that they caused confusion or were seen as inappropriate. Conclusions and Relevance This qualitative study found that when clinicians use emoji and emoticons in secure clinical texting systems, these symbols function primarily to convey new and interactionally salient information. These results suggest that concerns about the professionalism of emoji and emoticon use may be unwarranted.
Analysis of Breast Cancer Family History, Estrogen Receptor Status, and Breast Cancer Outcomes in Sweden
Authors: Yuqi Zhang, Qiao-Li Wang, Erwei Zeng, Wei He, Kamila Czene
Journal: JAMA Network Open (2023)

Importance Breast cancer (BC), the most prevalent cancer among women globally, is a heterogeneous disease, with prognosis differing by estrogen receptor (ER) status. Having a family history of BC increases the risk of BC; however, it is unclear whether family history is associated with the prognosis of overall and ER-specific BC. Objective To assess whether a family history of BC is associated with the prognosis of overall and ER-specific BC. Design, Setting, and Participants This cohort study was based on data from several national registers in Sweden. All female residents of Stockholm who were born after 1932; had their first BC diagnosis between January 1, 1991, and December 31, 2019; and had at least 1 identified female first-degree relative (FDR) were included. Women who were diagnosed with other types of cancer before their BC diagnosis, were older than 75 years at diagnosis, or had distant metastasis at diagnosis were excluded. A total of 28 649 women were included. Data were analyzed from January 10, 2022, to December 20, 2022. Exposures Family history of BC, defined as 1 or more female FDRs diagnosed with BC. Main Outcomes and Measures Patients were followed up until BC-specific death, censoring, or end of follow-up on December 31, 2019. The role of family history in BC-specific mortality was investigated using flexible parametric survival models among the full cohort, ER-positive subgroup, and ER-negative subgroup, adjusting for demographic characteristics, tumor characteristics, and treatments received. Results Among 28 649 patients, the mean (SD) age at BC diagnosis was 55.7 (10.4) years; 19 545 (68.2%) had ER-positive BC, and 4078 (14.2%) had ER-negative BC. Overall, 5081 patients (17.7%) had at least 1 female FDR diagnosed with BC, while 384 (1.3%) had a family history of early-onset BC (FDR diagnosed before age 40 years). During the follow-up period (median [IQR], 8.7 [4.1-15.1] years), 2748 patients (9.6%) died of BC. Multivariable analyses revealed that having a family history of BC was associated with a lower risk of BC-specific death among the full cohort (hazard ratio [HR], 0.78; 95% CI, 0.65-0.95) and the ER-negative subgroup (HR, 0.57; 95% CI, 0.40-0.82) in the first 5 years, after which no association was observed. However, having an early-onset family history was associated with a higher risk of BC-specific death (HR, 1.41; 95% CI, 1.03-2.34). Conclusions and Relevance In this study, patients with a family history of BC did not necessarily have a worse prognosis. Those with ER-negative status and a family history of BC had more favorable outcomes in the first 5 years after diagnosis, possibly due to enhanced motivation to receive and adhere to treatment. However, patients with a family history of early-onset BC had worse survival, suggesting that genetic testing of newly diagnosed patients with early-onset family history may provide useful information to aid treatment and future research.
CD8+ T cell depletion prevents neuropathology in a mouse model of globoid cell leukodystrophy
Authors: Pearl A. Sutter, Antoine Ménoret, Evan R. Jellison, Alexandra M. Nicaise, Allison M. Bradbury, Anthony T. Vella, Ernesto R. Bongarzone, Stephen J. Crocker
Journal: The Journal of Experimental Medicine (2023)

Globoid cell leukodystrophy (GLD) or Krabbe’s disease is a fatal genetic demyelinating disease of the central nervous system caused by loss-of-function mutations in the galactosylceramidase (galc) gene. While the metabolic basis for disease is known, the understanding of how this results in neuropathology is not well understood. Herein, we report that the rapid and protracted elevation of CD8+ cytotoxic T lymphocytes occurs coincident with clinical disease in a mouse model of GLD. Administration of a function-blocking antibody against CD8α effectively prevented disease onset, reduced morbidity and mortality, and prevented CNS demyelination in mice. These data indicate that subsequent to the genetic cause of disease, neuropathology is driven by pathogenic CD8+ T cells, thus offering novel therapeutic potential for treatment of GLD.
Access to Medically Necessary Reproductive Care for Individuals with Pulmonary Hypertension
Authors: Elizabeth Sonntag, Kathleen M. Akgün, Remzi Bag, Erika B. Rosensweig, Roberto J. Bernardo, Colleen Burnetti, Amy Chybowski, Vinicio A. de Jesus Perez, Johnell Diwan, Kate M. Guthrie, Torre Halscott, Tim Lahm, Jason Vaught, Corey E. Ventetuolo, Anna R. Hemnes
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Access to Medically Necessary Reproductive Care for Individuals with Pulmonary Hypertension." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Early Postnatal Ventricular Disproportion Predicts Outcome in Congenital Diaphragmatic Hernia
Authors: Flaminia Pugnaloni, Bartolomeo Bo, Lennart Hale, Irma Capolupo, Andrea Dotta, Pietro Bagolan, Lukas Schroeder, Christoph Berg, Annegret Geipel, Andreas Mueller, Neil Patel, Florian Kipfmueller
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Early Postnatal Ventricular Disproportion Predicts Outcome in Congenital Diaphragmatic Hernia." American Journal of Respiratory and Critical Care Medicine, 208(3), pp. 325–328
Cognitive impairment in people living with HIV: consensus recommendations for a new approach
Authors: Sam Nightingale, Beau Ances, Paola Cinque, Ameet Dravid, Anna J. Dreyer, Magnus Gisslén, John A. Joska, Judith Kwasa, Ana-Claire Meyer, Nombeko Mpongo, Noeline Nakasujja, Roger Pebody, Anton Pozniak, Richard W. Price, Christopher Sandford, Deanna Saylor, Kevin G. F. Thomas, Jonathan Underwood, Jaime H. Vera, Alan Winston
Journal: Nature Reviews Neurology (2023)
Chronic Rhinoviral Infection in Lung Transplant Recipients
Authors: Laurent Kaiser, John-David Aubert, Jean-Claude Pache, Christelle Deffernez, Thierry Rochat, Jorge Garbino, Werner Wunderli, Pascal Meylan, Sabine Yerly, Luc Perrin, Igor Letovanec, Laurent Nicod, Caroline Tapparel, Paola M. Soccal
Journal: American Journal of Respiratory and Critical Care Medicine (2006)

Rationale: Lung transplant recipients are particularly at risk of complications from rhinovirus, the most frequent respiratory virus circulating in the community.Objectives: To determine whether lung transplant recipients can be chronically infected by rhinovirus and the potential clinical impact.Methods: We first identified an index case, in which rhinovirus was isolated repeatedly, and conducted detailed molecular analysis to determine whether this was related to a unique strain or to re-infection episodes. Transbronchial biopsies were used to assess the presence of rhinovirus in the lung parenchyma. The incidence of chronic rhinoviral infections and potential clinical impact was assessed prospectively in a cohort of 68 lung transplant recipients during 19 mo by screening of bronchoalveolar lavages.Measurements and Main Results: We describe 3 lung transplant recipients with graft dysfunctions in whom rhinovirus was identified by reverse transcriptase–polymerase chain reaction in upper and lower respiratory specimens over a 12-mo period. In two cases, rhinovirus was repeatedly isolated in culture. The persistence of a unique strain in each case was confirmed by sequence analysis of the 5′NCR and VP1 gene. In the index case, rhinovirus was detected in the lower respiratory parenchyma. In the cohort of lung transplant recipients, rhinoviral infections were documented in bronchoalveolar lavage specimens of 10 recipients, and 2 presented with a persistent infection.Conclusions: Rhinoviral infection can be persistent in lung transplant recipients with graft dysfunction, and the virus can be detected in the lung parenchyma. Given the potential clinical impact, chronic rhinoviral infection needs to be considered in lung transplant recipients.
Endoscopic submucosal dissection assisted by adaptive traction: results of the first 54 procedures
Authors: Louis-Jean Masgnaux, Jean Grimaldi, Jérôme Rivory, Thierry Ponchon, Clara Yzet, Timothée Wallenhorst, Alexandru Lupu, Pierre Lafeuille, Romain Legros, Florian Rostain, Jérémie Jacques, Mathieu Pioche
Journal: Endoscopy (2023)

Background Good submucosal exposure is key to successful endoscopic submucosal dissection (ESD) and can be achieved with various traction devices. Nevertheless, these devices have a fixed traction force that tends to decrease as the dissection progresses. In contrast, the ATRACT adaptive traction device increases traction during the procedure. Methods In this retrospective analysis of prospectively collected data (from a French database), we analyzed ESD procedures performed with the ATRACT device between April 2022 and October 2022. The device was used consecutively whenever possible. We collected details of lesion characteristics, procedural data, histologic outcomes, and clinical consequences for the patient. Results 54 resections performed in 52 patients by two experienced operators (46 procedures) and six novices (eight procedures) were analyzed. The ATRACT devices used were the ATRACT-2 (n = 21), the ATRACT 2 + 2 (n = 30), and the ATRACT-4 (n = 3). Four adverse events were observed: one perforation (1.9 %), which was closed endoscopically, and three delayed bleeding events (5.5 %). The R0 rate was 93 %, resulting in curative resection in 91 % of cases. Conclusion ESD using the ATRACT device is safe and effective in the colon and rectum, but can also be used to assist with procedures in the upper gastrointestinal tract. It may be particularly useful in difficult locations.
Understanding the Physiological Endotypes Responsible for Comorbid Obstructive Sleep Apnea in Patients with Interstitial Lung Disease
Authors: Simon A. Joosten, Shane A. Landry, Dwayne L. Mann, Scott A. Sands, Christopher J. Ryerson, Calvin Sidhu, Garun S. Hamilton, Mark E. Howard, Bradley A. Edwards, Yet H. Khor
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Understanding the Physiological Endotypes Responsible for Comorbid Obstructive Sleep Apnea in Patients with Interstitial Lung Disease." American Journal of Respiratory and Critical Care Medicine, 208(5), pp. 624–627
A generalizable deep learning regression model for automated glaucoma screening from fundus images
Authors: Ruben Hemelings, Bart Elen, Alexander K. Schuster, Matthew B. Blaschko, João Barbosa-Breda, Pekko Hujanen, Annika Junglas, Stefan Nickels, Andrew White, Norbert Pfeiffer, Paul Mitchell, Patrick De Boever, Anja Tuulonen, Ingeborg Stalmans
Journal: npj Digital Medicine (2023)

A plethora of classification models for the detection of glaucoma from fundus images have been proposed in recent years. Often trained with data from a single glaucoma clinic, they report impressive performance on internal test sets, but tend to struggle in generalizing to external sets. This performance drop can be attributed to data shifts in glaucoma prevalence, fundus camera, and the definition of glaucoma ground truth. In this study, we confirm that a previously described regression network for glaucoma referral (G-RISK) obtains excellent results in a variety of challenging settings. Thirteen different data sources of labeled fundus images were utilized. The data sources include two large population cohorts (Australian Blue Mountains Eye Study, BMES and German Gutenberg Health Study, GHS) and 11 publicly available datasets (AIROGS, ORIGA, REFUGE1, LAG, ODIR, REFUGE2, GAMMA, RIM-ONEr3, RIM-ONE DL, ACRIMA, PAPILA). To minimize data shifts in input data, a standardized image processing strategy was developed to obtain 30° disc-centered images from the original data. A total of 149,455 images were included for model testing. Area under the receiver operating characteristic curve (AUC) for BMES and GHS population cohorts were at 0.976 [95% CI: 0.967-0.986] and 0.984 [95% CI: 0.980-0.991] on participant level, respectively. At a fixed specificity of 95%, sensitivities were at 87.3% and 90.3%, respectively, surpassing the minimum criteria of 85% sensitivity recommended by Prevent Blindness America. AUC values on the eleven publicly available data sets ranged from 0.854 to 0.988. These results confirm the excellent generalizability of a glaucoma risk regression model trained with homogeneous data from a single tertiary referral center. Further validation using prospective cohort studies is warranted.
Lung Function as a Biomarker of Health: An Old Concept Rediscovered
Authors: Myrtha E. Reyna, Marc-Antoine Bedard, Padmaja Subbarao
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Lung Function as a Biomarker of Health – An Old Concept Rediscovered." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Clinical Phenotype and Outcomes of Pulmonary Hypertension Associated with Myeloproliferative Neoplasms: A Population-based Study
Authors: David Montani, Pierre Thoré, Xavier Mignard, Xavier Jaïs, Athénaïs Boucly, Mitja Jevnikar, Andrei Seferian, Etienne-Marie Jutant, Vincent Cottin, Elie Fadel, Gérald Simonneau, Laurent Savale, Olivier Sitbon, Marc Humbert
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

Rationale: Precapillary pulmonary hypertension (PH) is a rare and largely unrecognized complication of myeloproliferative neoplasms (MPNs), including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (MF). Objectives: To describe characteristics and outcomes of MPN-associated PH. Methods: We report clinical, functional, and hemodynamic characteristics, classification, and outcomes of patients with PV, ET, or primary MF in the French PH registry. Measurements and Main Results: Ninety patients with MPN (42 PV, 35 ET, 13 primary MF) presented with precapillary PH with severe hemodynamic impairment, with a median mean pulmonary arterial pressure and pulmonary vascular resistance of 42 mm Hg and 6.7 Wood units, respectively, and impaired clinical conditions, with 71% in New York Heart Association functional classes III/IV and having a median 6-minute-walk distance of 310 m. Half of the patients were diagnosed with chronic thromboembolic PH (CTEPH); the other half were considered to have group 5 PH. MF was preferentially associated with group 5 PH, whereas PV and ET were generally related to CTEPH. Proximal lesions were diagnosed in half of the patients with CTEPH. Thromboendarterectomy was performed in 18 selected patients with high risk of complications (5 early deaths). Overall survival at 1, 3, and 5 years was 67%, 50%, and 34% in group 5 PH and 81%, 66%, and 42% in CTEPH, respectively. Conclusions: PH is a life-threatening condition potentially occurring in MPN. There are multiple mechanisms, with equal diagnoses of CTEPH and group 5 PH. Physicians should be aware that PH strongly affects the burden of patients with MPN, especially in group 5 PH, with unknown pathophysiological mechanisms.
Right Ventricular Response to Acute Hypoxia among Healthy Humans
Authors: Lindsay M. Forbes, Todd M. Bull, Tim Lahm, Justin S. Lawley, Kendall Hunter, Benjamin D. Levine, Andrew Lovering, Robert C. Roach, Andrew W. Subudhi, William K. Cornwell
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

indicating that subphenotype assignment also has strong prognostic relevance in children with ARF but not PARDS.Recent investigations in adults with ARF without ARDS also support the existence of two subphenotypes with characteristics similar to those seen in patients with ARDS, again distinguishable by inflammatory biomarkers and by clinical outcomes (5, 8).Thus, these two subphenotypes share overlap across the adult and pediatric ARF spectra, offering a rationale for innovative trial enrollment strategies across ages.Our findings emphasize the challenge of syndromic definitions such as PARDS in specific, and ARF in general, which struggle to identify and characterize complex pathophysiologic processes that culminate from multiple inciting diagnoses.Our data suggest that the complex inflammatory pathways and inflammatory-related subphenotypes associated with PARDS (3, 9) are also involved in children with ARF, and recent data suggest that they may also be observed in other critically ill children (10).In conclusion, these data suggest that parsimonious model subphenotype assignment can enable robust prognostic enrichment compared with prior risk stratification schema.Earlier identification of high-risk subphenotypes, particularly in pediatric patients, could result in earlier escalation of care in patients at greater risk for complex course.After validation, these data may impact future clinical trial design, including the expansion of subphenotype identification to the broader pediatric ARF cohort.
Cardiovascular Disease and Chronic Obstructive Pulmonary Disease: Adding a Third Dimension to the ABE Global Initiative for Chronic Obstructive Lung Disease 2023 Chronic Obstructive Pulmonary Disease Classification
Authors: Konstantinos Kostikas, Athena Gogali, Georgios Hillas
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Cardiovascular Disease and COPD: Adding a Third Dimension to the ABE GOLD 2023 COPD Classification." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Sleep Apnea and Chronic Obstructive Pulmonary Disease Overlap: More Common Than You Think?
Authors: Janna R. Raphelson, Ana Sanchez-Azofra, Atul Malhotra
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Sleep Apnea and COPD Overlap: More Common Than You Think?." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Postextubation Noninvasive Respiratory Support in Patients with Acute Brain Injury: Not a Panacea, but Don’t Throw the Baby Out with the Bathwater!
Authors: Romain Pirracchio, Alejandro A. Rabinstein
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Post-Extubation Non-Invasive Respiratory Support in Patients with Acute Brain Injury: Not a Panacea but Don’t Throw the Baby Out with the Bathwater!." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.